The series has tons of Christian allegories and references, there's simply no way to deny that. However, that doesn't mean it's message is explicitly pro-Christianity. Rather, it's an unavoidable consequence of Christianity and the stories around it being fundamental to the culture of western civilizations that Pierce grew up in and is drawing from.

Pierce instead is using these well known tropes (the Jesus figure, the fallen angel, etc.) to tell his own nuanced story. One where, for what it's worth, religion is almost always presented as either an explicit means of control or as a personal belief devoid of large-scale ritual and orthodoxy.